Dynamic covalent self-assembly and self-sorting processes in the formation of imine-based macrocycles and macrobicyclic cages

Key structural features to favour imines over hydrates in water: pyridoxal phosphate as a muse

Imination reactions in water represent a challenge not only because of the high propensity of imines to be hydrolysed but also as a result of the competing hydrate formation through H2O addition to the aldehyde. In the present work we report a successful approach that allows for favouring imitation reactions while silencing hydrate formation. Such remarkable reactivity and selectivity can be attained by fine-tuning the electronic and steric structural features of the ortho-substituents of the carbonyl groups. It resulted from studying the structure-reactivity relationships in a series of condensation reactions between different amines and aldehydes, comparing the results to the ones obtained in the presence of the biologically-relevant pyridoxal phosphate (PLP). The key role of negatively-charged and sterically-crowding units (i.e., sulfonate groups) in disfavouring hydrate formation was corroborated by DFT and steric-hindrance calculations. Furthermore, the best-performing aldehyde leads to higher imine yields, selectivity and stability than those of PLP itself, allowing for the inhibition of a PLP-dependent enzyme (transaminase) through dynamic aldimine exchange. These results will increase the applicability of imine-based dynamic covalent chemistry (DCvC) under physiological conditions and will pave the way for the design of new carbonyl derivatives that might be used in the dynamic modification of biomolecules.

Social Self-Sorting of Quasi-Racemates: A Unique Approach for Dual-Pore Molecular Crystals

Despite recent advances in porous organic molecular crystals, the engineering of dual-pore systems within the intermolecular voids remains a significant challenge. In this study, we have achieved the crystallization-induced social self-sorting of "quasi-racemic" dialdehydes into a macrocyclic imine. X-ray crystallographic analysis unambiguously characterizes the resulting structure as incorporating two quasi-racemate pairs with four diamine molecules. Notably, different alkyl substituents on the quasi-racemates afford two types of one-dimensional pores within the macrocyclic imine crystal. The different adsorption properties of these pores were substantiated through adsorption experiments. An intriguing helical arrangement of guest molecules was observed within one of the pores. This study provides pioneering evidence that the social self-sorting of quasi-racemates offers a new methodology for creating dual-functional supramolecular materials.

Triply Adaptive Libraries of Dynamic Covalent Macrocycles: Switching between Sorted and Unsorted States

Dynamic noncovalent and covalent chemistries have enabled the constitutional modulation of chemical entities within chemical dynamic systems. The switching between order and disorder, i.e., self-sorted and unsorted states of constitutional dynamic libraries, remains challenging. Herein, we study the adaptive behaviors of a dynamic library of imine macrocycles generated from dialdehydes and diamines, seeking ways to exert control over sorting and unsorting processes. The distribution of constituents in the present library of dynamic macrocycles is modulated in response to internal and external effectors (e.g., time, metal cations, and chemical fuels), resulting in the transient amplification of self-sorted constituents in out-of-equilibrium states. The present study showcases higher complexity in systems subject to multiple adaptation through the dynamic interconversion between singularity/order and diversity/disorder.

Uncovering tetrazoles as building blocks for constructing discrete and polymeric assemblies

Metal-organic self-assembly with flexible moieties is a budding field of research due to the possibility of the formation of unique architectures. Tetrazole, characterised by four nitrogen atoms in a five-member ring, exhibits immense potential as a component. Tetrazole offers four coordination sites for binding to the metal centre with nine distinct binding modes, leading to various assemblies. This review highlights different polymeric and discrete tetrazole-based assemblies and their functions. The meticulous manipulation of stoichiometry, ligands, and metal ions required for constructing discrete assemblies has also been discussed. The different applications of these architectures in separation, catalysis and detection have also been accentuated. The latter section of the review consolidates tetrazole-based cage composites, highlighting their applications in cell imaging and photocatalytic applications.

Constitutional adaptation to pKa modulation by remote ester hydrolysis

The mechanisms through which environmental conditions affect the expression of interconnected species is a key step to comprehending the principles underlying complex chemical processes. In Nature, chemical modifications triggered by the environment have a major impact on the structure and function of biomolecules and regulate different reaction pathways. Yet, minimalistic artificial systems implementing related adaptation behaviours remain barely explored. The hydrolysis of amino acid methyl esters to their corresponding amino acids leads to a drastic change in pKa (ca. 7 and 9, respectively) that protonates the free amino group at physiological conditions. Dynamic covalent libraries (DCvLs) based on amino acid methyl esters and aldehydes respond to such hydrolysis and lead to constitutional adaptation. Each of the libraries studied experiences a DCvL conversion allowing for constituent selection due to the silencing of the zwitterionic amino acids towards imine formation. The selective action of different enzymes on the DCvLs results in states with simplified constitutional distributions and transient chirality. When additional components (i.e., scavengers) that are not affected by hydrolysis are introduced into the dynamic libraries, the amino acid methyl ester hydrolysis induces the up-regulation of the constituents made of these scavenging components. In these systems, the constituent distribution is resolved from a scrambled mixture of imines to a state characterized by the predominance of a single aldimine. Remarkably, although the final libraries display higher "simplexity", the different transient states present an increased complexity that allows for the emergence of organized structures [micelle formation] and distributions [up-regulation of two antagonistic constituents]. This reactive site inhibition by a remote chemical modification resembles the scenario found in some enzymes for the regulation of their activity through proximal post-translational modifications.

Stabilization of Lantern-Type Metal-Organic Cages (MOCs) by Protective Control of Ligand Exchange Rates

Self-assembling systems in nature display remarkable complexity with assemblies of different sub-units to generate functional species. Synthetic analogues of such systems are a challenge, often requiring the ability to bias distributions that are under thermodynamic assembly control. Using lantern-type MOCs (metal-organic cages) as a prototypical self-assembling system, herein we explore the role that steric bulk plays in controlling the exchange rate of ligands in paddlewheel-based assemblies, and thus the stability of cages, in competitive self-assembling scenarios. The effective lifetime of the lantern-type MOCs varies over an order of magnitude depending on the steric bulk proximal to the metal nodes with lifetimes of the cages ranging from tens of minutes to several hours. The bulk of the coordinating solvents likewise reduces the rate of ligand exchange, and thus yields longer-lived species. Understanding this subtle effect has implications for controlling the stability of complex assemblies in competitive environments with implications for guest release and application.

Development of Receptor for Advanced Glycation End Products (RAGE) ligands through target directed dynamic combinatorial chemistry: a novel class of possible antagonists

RAGE is a transmembrane receptor of immunoglobulin family that can bind various endogenous and exogenous ligands, initiating the inflammatory downstream signaling pathways, including inflammaging. Therefore, RAGE represents an attractive drug target for age-related diseases. For the development of small-molecule RAGE antagonists, we employed protein-templated dynamic combinatorial chemistry (ptDCC) using RAGE's VC1 domain as a template, the first application of this approach in the context of RAGE. The affinities of DCC hits were validated using microscale thermophoresis. Subsequent screening against AGE2 (glyceraldehyde-modified AGE)-sRAGE (solubleRAGE) (AGE2-BSA/sRAGE) interaction using ELISA tests led to the identification of antagonists with micromolar potency. Our findings not only demonstrate the successful application of ptDCC on RAGE but also highlight its potential to address the pressing need for alternative strategies for the development of small-molecule RAGE antagonists, an area of research that has experienced a slowdown in recent years.

Heteromeric Completive Self-Sorting in Coordination Cage Systems

Heteroleptic coordination cages, nonstatistically assembled from a set of matching ligands, can be obtained by mixing individual components or via cage-to-cage transformations from homoleptic precursors. Based on the latter approach, we here describe a new level of self-sorting in coordination cage systems, namely, 'heteromeric completive self-sorting'. Here, two heteroleptic assemblies of type Pd2A2B2 and Pd2A2C2, sharing one common ligand component A but differing in the other, are shown to coexist in solution. This level of self-sorting can be reached either from a statistical mixture of assemblies based on some ligands B and C or, alternatively, following a first step of integrative self-sorting giving a distinct Pd2B2C2 intermediate. While subtle enthalpic factors dictate the outcome of the self-sorting, we found that it is controllable. From a unique set of three ligands, we demonstrate the transition from strict integrative self-sorting forming a Pd2AB2C cage to heteromeric completive self-sorting to give Pd2A2B2 and Pd2A2C2 by variation of the ligand ratio. Cage-to-cage transformations were followed by NMR and MS experiments. Single crystal X-ray structures for three new heteroleptic cages were obtained, impressively highlighting the versatility of ligand A to either form a π-stacked trans-figure-of-eight arrangement in Pd2A2B2 or occupy two cis-edges in Pd2A2C2 or only a single edge in Pd2AB2C. This study paves the way toward the control of heteroleptic cage populations in a systems chemistry context with emerging features such as chemical information processing, adaptive guest selectivity, or stimuli-responsive catalytic action.

Dynamic covalent synthesis

Dynamic covalent synthesis aims to precisely control the assembly of simple building blocks linked by reversible covalent bonds to generate a single, structurally complex, product. In recent years, considerable progress in the programmability of dynamic covalent systems has enabled easy access to a broad range of assemblies, including macrocycles, shape-persistent cages, unconventional foldamers and mechanically-interlocked species (catenanes, knots, etc.). The reversibility of the covalent linkages can be either switched off to yield stable, isolable products or activated by specific physico-chemical stimuli, allowing the assemblies to adapt and respond to environmental changes in a controlled manner. This activatable dynamic property makes dynamic covalent assemblies particularly attractive for the design of complex matter, smart chemical systems, out-of-equilibrium systems, and molecular devices.

Cavity-Shape-Dependent Divergent Chemical Reaction inside Aqueous Pd6L4 Cages

Chemical reactions inside the confined pockets of enzyme-mimicking hosts, such as cages and macrocycles, have been an emerging field of interest over the past decade. Although many such reactions are known, the use of such cages toward the divergent synthesis of nonisomeric products has not been well explored. Divergent synthesis is a technique of forming two or more distinct products from the same reagents by changing the catalyst or reaction conditions. Changing the shape of the cage can also change the nature and magnitude of the host-guest interactions. Thus, is it possible for such changes to cause differences in the reaction pathways leading to formation of nonisomeric products? Herein, we report a divergent chemical transformation of anthrone [anthracen-9(10H)-one] inside different water-soluble M6L4 cages. When anthrone was encapsulated inside a newly synthesized M6L4 octahedral cage 1, it dimerized to form dianthrone [9,9'-bianthracen-10,10'(9H,9'H)-dione]. In contrast, when the same chemical reaction was performed inside a M6L4 double-square shaped cage 2, it was oxidized to form anthraquinone [anthracene-9,10-dione]. Similar results were obtained with a different set of isomeric aqueous Pd6 cages 3a (octahedral cage) and 3b (double-square cage), indicating the dependence of the shape of cavity on the divergent synthesis. The present report demonstrates a unique example of different outcomes/results of a reaction depending on the shape of the molecular container, which was driven by the host-guest interactions and the preorganization of the substrates.

Recent applications of organic cages in sensing and separation processes in solution

Organic cages are three-dimensional polycyclic compounds of great interest in the scientific community due to their unique features, which generally include simple synthesis based on the dynamic covalent chemistry strategies, structural tunability and high selectivity. In this feature article, we present the advances over the last ten years in the application of organic cages as chemosensors or components in chemosensing devices for the determination of analytes (pollutants, analytes of biological interest) in complex aqueous media including wine, fruit juice, urine. Details on the recent applications of organic cages as selective (back-)extractants or masking agents for potential applications in relevant separation processes, such as the plutonium and uranium recovery by extraction, are also provided. Over the last ten years, organic cages with permanent porosity in the liquid and solid states have been highly appreciated as porous materials able to discriminate molecules of different sizes. These features, combined with good solvent processability and film-forming tendency, have proved useful in the fabrication of membranes for gas separation, solvent nanofiltration and water remediation processes. An overview of the recent applications of organic cages in membrane separation technologies is given.

Highly Efficient One-Pot Synthesis of Hexakis(m-phenyleneimine) Macrocyle Cm6 and the Thermostimulated Self-Healing Property through Dynamic Covalent Chemistry

Highly efficient one-pot synthesis of hexakis(m-phenyleneimine) macrocycle Cm6 from acetalprotected AB-type monomer, m-aminobenzaldehyde diethylacetal, was successfully achieved based on imine dynamic covalent chemistry and precipitation-driven cyclization. The structure of Cm6 in the solid state was determined using CP/MAS NMR, X-ray single crystallographic analysis, and WAXD. Macrocycle Cm6 is composed of six phenylene and imine bonds facing the same direction, with nitrogen atoms arranged on the outside of the ring, and has a chair conformation, as predicted from DFT calculation. The macrocycle forms π-stacked columnar aggregates and hexagonally closest-packed structure. The cyclization process was investigated using MALDI-TOF MS and NMR. A mechanism of precipitation-driven cyclization based on imine dynamic covalent chemistry and π-stacked columnar aggregation is proposed. Both the nature of imine linkage and the shape anisotropy of the macrocycle played an important role in the single one-pot synthesis. The water-mediated mutual conversion between macrocycle Cm6 and linear oligomers driven by thermal stimulation was analyzed using MALDI-TOF MS and GPC methods. Macrocycle Cm6 with a dynamic covalent imine bond exhibited self-healing properties when stimulated using heat.